The Norwegian Atlantic Current (NwAC) as a poleward eastern boundary current is to be considered as the northern limb of the Meridional Overturning Circulation in the North Atlantic (MOC). It transports warm and saline Atlantic water (AW) northward toward the Arctic Ocean, before cooling and mixing with cold and low saline water masses return it to the North Atlantic to contribute in the MOC. In this study we focus on the AW in the Lofoten Basin (LB) of the Norwegian Sea (NS), where it occupies a wider and deeper domain than farther south and north. It comprises the major heat-reservoir in the NS with contact with the atmosphere, and as such is an important area for cooling and buoyancy loss. We show that the deepening of the AW is mainly caused by the reduced northward flow in the LB, manifested in the deep counter-current encountered by the Polar frontal jet. We demonstrate this effect by using an active reduced gravity model with a topographically-steered deeper flow. To achieve maintenance of volume transport, the model shows that observed differences must be balanced by an oppositely-directed deeper flow in the LB. The ocean appears to achieve maintenance of volume transport of AW due to buoyancy loss and varying deeper currents, by adjusting the vertical extension of AW, resulting in a substantial deepening in the LB. Based on the good fit between the model and observations, the suggested mechanism appears to be credible and feasible.